Operation Atlantis
by GoldenChocobo
Summary: Someone is close enough to Shepard to know his weaknesses. Someone is close enough to cripple his defences. Someone is close enough to stop him winning the war. But one slip up could cause their plan to crumble. AU MShep Sentinel/Spacer/Sole Survivor. Rated M for language. Features various characters from the universe. (Not Slash)
1. Chapter I : Hermes

Operation Atlantis

Chapter I : Hermes

The door to the Normandy's elevator slid open and Commander Shepard took several steps out when Specialist Traynor walked over to greet him.

''Shepard, we've improved the Normandy's thrust capacity by 4.28% and you've got a message flagged urgent on your private terminal.''

''Great work Traynor, it's great to see you and EDI working well together after… you know… the party." Shepard slowed to an awkward stop.

''Thanks Shepard, you know how to make things really awkward.'' Traynor laughed awkwardly.

''Specialist Traynor has been showing higher signs of discomfort. She needn't be awkward around me, I find her attraction… flattering.'' EDI spoke over the comms.

''Yes… thank you EDI.'' Traynor replied, blushing. ''I'll just be… over here…''

Shepard approached his private terminal and read the urgent message.

_Shepard I have an important issue to talk to you about. Could I see you in your cabin? EDI._

Shepard looked around the CIC, confused as to why EDI had sent him the message rather than asked. He headed for the elevator and took it up to his cabin. After almost 2 minutes in the elevator the doors slid open and he proceeded to walk to his cabin. The cabin door slid open and he was greeted by EDI.

''Hello, Shepard. I'm glad you came.'' EDI smiled.

''You had something you wanted to talk to me about?''

''Yes,'' EDI seemed to hesitate, ''I found this bug under your desk when I scanned your cabin.''

''A bug?'' Shepard was confused as EDI passed him a small circular device.

''I believe one of the crew are working against us, against you.'' EDI announced, holding her head higher as she held her hands behind her back.

''What? How do you know?'' Shepard's jaw dropped.

''I intercepted an encrypted message that was sent to an omni tool aboard the Normandy. I, however, cannot use the message to track the receiver.''

''What did the message say?'' Shepard walked over to his sofa and sat down, still holding the bug. EDI followed the Commander and also sat down.

''Commander Shepard is rallying the other races, the time to act is now. Begin Operation Atlantis and remove him.''

A few moments passed in silence as the news sank in.

''What do I do EDI? Who can I trust?'' Shepard placed the bug on the table and held his head in his hands.

''The bug was placed recently, so you can rule out Joker, I've been with him constantly, the retrofitting crew and anyone that hasn't been to the Normandy.'' EDI paused and stared at Shepard. ''I'm sorry Shepard… this must be difficult.''

''Thanks EDI,'' He looked at her. ''Who sent the message?''

''I had to use my most advanced techniques to decrypt the message, techniques I learned through the Reaper Code.'' EDI paused once again. ''I believe it was the Reapers, for them to send a message… you must be a significant concern for them.''

''The Reapers… someone aboard the ship is indoctrinated…'' Shepard stood up and paced. ''Well we can rule out any alien race right? Atlantis is a Greek human myth.''

''You are correct, but the name of an operation doesn't rule out any race.'' EDI replied.

''We need to dock at the Citadel, I need to speak to someone.'' Shepard announced, grabbing the bug and leaving the room.

...

Shepard walked up towards the bridge to see Joker, EDI followed quickly behind.

''Joker'' Shepard spoke, ''set a course for the Citadel, I have to talk to someone.''

''Aye aye, Commander… I'm guessing EDI told you?'' Joker tapped several areas on the screen and turned the pilot seat around.

''Yes, it's nice to know there is someone on my ship I can completely trust… but this can't be happening.'' Shepard frowned as he shook his head.

''Nothing has happened yet Shepard, it's just a message.'' Joker held up his hands to try and calm the Commander.

''Still… someone on this ship has betrayed the Galaxy, they've betrayed Earth…'' Shepard inhaled sharply, ''they've betrayed me… I don't think I can take much more of this Joker… this war.''

''I know Shepard, get some rest. We'll be at the Citadel soon enough.'' Joker span his chair back around and EDI sat beside him. Shepard turned around and walked away. Shepard was walking through the CIC, when Kaidan called him over.

''Not tonight Kaidan, I need to think something through, you and Garrus have a good time without me.'' Shepard waved him off, not even allowing him to talk; Shepard stalked to the elevator and rode it up to his cabin.

Kaidan glared after the Commander for a while until Garrus came over to interrupt him.

''What was that about?'' Garrus asked. Kaidan waited a moment before responding.

''Something's riled him.''


	2. Chapter II : Ares

Operation Atlantis

Chapter II : Ares

Garrus ran up to Kaidan as the crew were leaving the Normandy.

''Shore leave? Already?'' Garrus asked, catching his breath. Kaidan nodded. ''Shouldn't we be heading after Kai Leng?''

''I know.'' Kaidan agreed, he wasn't in the best of moods. ''Seems as we have shore leave, we might as well enjoy it.''

''Purgatory?'' Garrus asked, almost as if reading Kaidan's mind.

''Took the words right out of my mouth.'' He replied.

...

''Shepard, over here!'' Miranda called as she saw the Commander arrive at the bank on the presidium. She waved him to come over. She was leaning on a rail looking out over the presidium.

''Miranda,'' Shepard spoke as he finished jogging over to her, ''Where's Jack?''

''Late, obviously, remind me why you called her?'' Miranda asked sarcastically. Shepard ignored her question and presented the bug to Miranda.

''This better be important… you should be chasing Kai Leng right to the Illusive man…'' She sighed. ''So a bug? Hmm… it's pretty high tech, it is able to connect to comm buoys and send recordings across the galaxy, stolen no doubt. I remember ordering some like these during the Lazarus Project; I had some doubts about my cell.'' Miranda spoke as she analysed the device. ''The manufacturer, a Volus company called Elasrik Securities; they were bought out about a year ago, just after I placed my order. They never resurfaced; I assumed they were broken down into smaller companies to be sold off.''

''No chance of tracking a stolen shipment then?'' Shepard asked hopefully.

''I can answer that.'' Jack interrupted.

''Jack?'' Shepard replied.

''Hello Shepard… Miranda.'' Jack spoke as she snatched the device from Miranda's hand.

''A device this high tech, the thief would never allow themselves to be tracked they'd probably use various software to cover their tracks.'' Jack spoke, looking at the device. Miranda and Shepard looked at her oddly; she looked at them confused. ''What? I was a pirate once.''

''Well judging by your face, I can see you're accustomed to small things. But I only had to look at your chest to confirm that.'' Miranda mocked, not to be out done by the former criminal.

''Your ego, ass and tit's may be bigger than mine, but your tiny shrivelled ovaries show who's more of a woman, bitch.'' Jack responded just as fast.

''How…?'' Miranda was lost for words, unsure how this personal information got to Jack.

''You, me and every embarrassing little secret.'' Jack mocked, she winked at Miranda. Miranda rolled her eyes in response.

''Guys!'' Shepard grew impatient. ''This is important.''

''It's okay Shepard… it's just harmless fun.'' Jack smirked.

''Yes… harmless…'' Miranda replied, glaring down the tattooed woman.

''Look the Normandy has eyes and ears aboard, but the Citadel has more. Report to the Normandy, we can continue there.''

''Great, I'm joining back up with the girl scouts. See you later.'' Jack wandered off after tossing the device to Shepard.

''I just have to take care of Oriana, I'll be at the Normandy shortly.'' Miranda replied walking off.

...

''Shepard is on to you,'' A deep metallic voice bellowed, ''He has somehow intercepted and decrypted the message we sent.''

A hooded figure stood in one of the dark passages that dotted the Citadel, their omni-tool projected the hologram of a Reaper.

''How…? Shepard doesn't even…'' The figure cut off as a wave of realisation washed over them, ''of course… his AI, EDI, it must have utilised the Reaper code.''

''Yet again, organics prove what we already know. They are inferior.''

''Before you blame this on me, I was kept away from Shepard during the Collector abductions, in which you were bested by organics, so I had no intelligence on the AI!'' The figure argued.

''Enough!'' The Reaper bellowed, ''in time you will understand that your destruction is inevitable, your only salvation is found with us.''

...

''Commander, Jack and Miranda are here, should I put away anything breakable?'' Joker buzzed over the comms.

''It's okay Joker, send them up.'' Shepard replied.

''Aye aye.''

A few minutes later the door to Shepard's cabin slid open. Miranda stepped through, followed by Jack.

''Hello Shepard.'' Miranda smiled, walking passed him and sitting down at his desk.

''Hey.'' Jack uttered as she wandered passed Shepard and dove onto his bed. ''Wow! This bed is great!''

''Uh… Hi you two.'' Shepard was mildly surprised by the fact that time hadn't changed how comfortable his former crew mates were with him.

''So what's the plan?'' Miranda said, spinning the chair around to look at Shepard.

''As the security company is our only lead at this time, we may as well look them up and see what we can dig up.'' Shepard rubbed the back of his neck as he headed to the sofa. Miranda stood up and followed. She walked down the steps, heading for the sofa.

''I'll handle that.'' Miranda volunteered.

''Hey Cerberus Cheerleader, the last time you said you could handle something, you got Jacob carried off by a seeker swarm.''


End file.
